Biomolecular Structure Prediction Stochastic Optimization Methods

Abstract Biomolecular structure prediction remains an important challenge to biophysical chemistry. We recently developed an all‐atom free energy forcefield (PFF01) for protein structure prediction with stochastic optimization methods. We review recent studies, which demonstrated all‐atom folding of several proteins and summarize recent progress for in‐silico high‐throughput screening strategies for rational drug design, which are also based on the use of stochastic optimization methods to determine the conformation of the receptor‐ligand complex.